SMTL ID : 2c5h.1

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

4 x MET: METHIONINE(Non-covalent)

MET.1: 11 residues within 4Å: Chain A: D.210, F.213, W.217, S.269, R.270 Chain C: L.17, D.21, S.23, T.155, F.156 Ligands: 3D1.5 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.17, C:F.156 Hydrogen bonds: C:S.23, A:D.210, A:S.269, A:S.269 Salt bridges: A:R.270 MET.4: 12 residues within 4Å: Chain A: L.17, D.21, S.23, T.155, F.156 Chain B: D.210, F.213, N.215, W.217, S.269, R.270 Ligands: 3D1.2 7 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.156 Hydrogen bonds: A:D.21, A:S.23, B:D.210, B:S.269, M.4 Salt bridges: B:R.270 MET.7: 11 residues within 4Å: Chain D: D.210, F.213, W.217, S.269, R.270 Chain F: L.17, D.21, S.23, T.155, F.156 Ligands: 3D1.11 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:L.17, F:F.156 Hydrogen bonds: F:S.23, D:D.210, D:S.269, D:S.269 Salt bridges: D:R.270 MET.10: 12 residues within 4Å: Chain D: L.17, D.21, S.23, T.155, F.156 Chain E: D.210, F.213, N.215, W.217, S.269, R.270 Ligands: 3D1.8 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: E:D.210, E:S.269, D:D.21, D:S.23, M.10 Salt bridges: E:R.270 Hydrophobic interactions: D:F.156

6 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)

3D1.2: 20 residues within 4Å: Chain A: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain B: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 Ligands: MET.4 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.77, A:T.80, A:S.158, A:S.158, A:S.158, B:N.215, B:R.277, B:A.279 Hydrophobic interactions: B:F.213 pi-Stacking: B:F.213, B:F.254, B:F.254 3D1.5: 18 residues within 4Å: Chain A: F.213, N.215, F.254, R.277, N.278, A.279, A.280 Chain C: D.16, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Ligands: MET.1 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:F.213 Hydrogen bonds: A:N.215, A:R.277, A:A.279, C:Y.77, C:T.80, C:Y.157, C:S.158, C:S.158, C:S.158 pi-Stacking: A:F.254, A:F.254, C:W.50, C:W.50 3D1.6: 19 residues within 4Å: Chain B: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain C: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:Y.77, B:S.158, B:S.158, B:S.158, C:N.215, C:R.277, C:A.279 pi-Stacking: B:W.50, B:W.50, B:W.50, B:W.50, C:F.254, C:F.254 Hydrophobic interactions: C:F.213 3D1.8: 20 residues within 4Å: Chain D: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain E: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 Ligands: MET.10 11 PLIP interactions: 7 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:F.213 Hydrogen bonds: E:N.215, E:R.277, E:A.279, D:Y.77, D:S.158, D:S.158, D:S.158 pi-Stacking: E:F.213, E:F.254, E:F.254 3D1.11: 18 residues within 4Å: Chain D: F.213, N.215, F.254, R.277, N.278, A.279, A.280 Chain F: D.16, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Ligands: MET.7 14 PLIP interactions: 8 interactions with chain F, 6 interactions with chain D Hydrogen bonds: F:T.76, F:Y.77, F:Y.157, F:S.158, F:S.158, F:S.158, D:N.215, D:R.277, D:A.279 pi-Stacking: F:W.50, F:W.50, D:F.254, D:F.254 Hydrophobic interactions: D:F.213 3D1.12: 19 residues within 4Å: Chain E: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain F: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 14 PLIP interactions: 8 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:Y.77, E:S.158, E:S.158, E:S.158, F:N.215, F:R.277, F:A.279 pi-Stacking: E:W.50, E:W.50, E:W.50, E:W.50, F:F.254, F:F.254 Hydrophobic interactions: F:F.213

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mcewan, A.R. et al., Substrates and Inhibitors of the Fluorinase from Streptomyces Cattleya. To be Published

Release Date

2006-10-25

Peptides

5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE

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